5KCT: ER-alpha Ligand-binding Domain

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an N-ethyl, 4-chlorobenzyl OBHS-N derivative. Determined by X-ray diffraction at 1.6 Å resolution. Released 16 Nov 2016.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,306
Mol. weight: 62.93 kDa
Ligands: OB6, OB7
Released: 16 Nov 2016

Explore 5KCT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KCT contains 25 α-helices and 4 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	306-309	4
α-helix	312-322	11
α-helix	323-328	6
α-helix	339-361	23
α-helix	367-369	3
α-helix	372-394	23
β-strand	401-405	5	1
β-strand	408-411	4	1
α-helix	412-415	4
α-helix	421-437	17
α-helix	442-455	14
α-helix	473-492	20
α-helix	497-531	35
α-helix	538-545	8

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	307-309	3
α-helix	312-321	10
α-helix	323-328	6
α-helix	339-361	23
α-helix	367-369	3
α-helix	372-394	23
β-strand	401-405	5	2
β-strand	408-411	4	2
α-helix	422-437	16
α-helix	442-455	14
α-helix	469-492	24
α-helix	497-525	29
α-helix	538-545	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	689-693	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	689-695	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Estrogen receptor	A, B	protein	257	Homo sapiens	P03372 (AlphaFold model)
NCOA2	C, D	protein	14	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5KCT_1 Estrogen receptor (chains A, B)
IKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHM
INWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKC
VEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHR
VLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLS
DLLLEMLDAHRLHAPTS

Sequence of entity 2 (C, D), FASTA

>5KCT_2 NCOA2 (chains C, D)
KHKILHRLLQDSSS

Ligands and cofactors

ID	Name	Formula	Copies
OB6	(1S,2R,4S)-N-(4-chlorophenyl)-N-ethyl-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2…	C26 H24 Cl N O5 S	1
OB7	(1R,2S,4R)-N-(4-chlorophenyl)-N-ethyl-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2…	C26 H24 Cl N O5 S	1

Primary citation

Full antagonism of the estrogen receptor without a prototypical ligand side chain. Srinivasan, S., Nwachukwu, J.C., Bruno, N.E. et al. Nat Chem Biol (2017) 13:111-118. DOI 10.1038/nchembio.2236 · PubMed

Other PDB entries of the same protein (UniProt P03372 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BAA 1.1 Å, Cys-42-tethered stabilizer 12 of 14-3-3(sigma)/ERa PPI
8BZC 1.1 Å, co-soaked stabilizers for ERa - 14-3-3 interaction (884_AZ244)
8BZW 1.1 Å, Co-soaked stabilizers for ERa - 14-3-3 interaction (844_AZ210)
8C04 1.1 Å, Co-soaked stabilizers for ERa - 14-3-3 interaction (884_AZ354)
7B9R 1.15 Å, Cys-45-tethered stabilizer 4 of 14-3-3(sigma)/ERa PPI
7B9T 1.15 Å, Cys-45-tethered stabilizer 5 of 14-3-3(sigma)/ERa PPI
7NFW 1.19 Å, Human 14-3-3 sigma in complex with human Estrogen Receptor alpha peptide
6HMU 1.2 Å, Ternary complex of Estrogen Receptor alpha peptide and 14-3-3 sigma C45 mutant bound to…
7BA8 1.2 Å, Cys-42-tethered stabilizer 10 of 14-3-3(sigma)/ERa PPI
8APS 1.2 Å, Small molecular stabilizer for ERalpha and 14-3-3 (1083744)
8BX3 1.2 Å, fragment-linked stabilizer for ERa - 14-3-3 interaction (1074372)
8BXI 1.2 Å, fragment-linked stabilizer for ERa - 14-3-3 interaction (1074361)

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